Showing : go • reset
2
votes
2
replies
2.5k
views
Converting single GRanges object as per chromosome GRangeList
SNP GO convert SNP GO convert
updated 11.9 years ago by ★ 13k • written 11.9 years ago by ▴ 260
0
votes
1
reply
2.3k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 11.9 years ago by ▴ 80 • written 11.9 years ago by ▴ 20
0
votes
0
replies
1.5k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
11.9 years ago Nicolas Delhomme ▴ 320
0
votes
1
reply
1.8k
views
GOSemSim function, clusterSim throws expired SQLiteConnection error
GO GOSemSim GO GOSemSim
updated 12.0 years ago by ★ 1.2k • written 12.0 years ago by ★ 13k
0
votes
2
replies
1.9k
views
Question about ReportingTools used with DESeq2
GO BSgenome BSgenome ReportingTools DESeq2 GO BSgenome BSgenome ReportingTools DESeq2
updated 12.0 years ago by 68k • written 12.0 years ago by ▴ 80
0
votes
5
replies
2.6k
views
Graph of methylation data around TSS - Repitools or other package?
GO Repitools GO Repitools
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ★ 1.1k
0
votes
2
replies
1.2k
views
DEXSeq package: plotDEXSeq for multiple conditions
GO GO
updated 12.0 years ago by ★ 1.9k • written 12.0 years ago by ▴ 230
0
votes
2
replies
4.6k
views
Gene filtering for RNA-seq data
Normalization GO Network HTSFilter DESeq2 Normalization GO Network HTSFilter DESeq2
updated 12.0 years ago by 43k • written 12.0 years ago by ★ 13k
0
votes
7
replies
2.8k
views
methyAnalysis error
GO convert methylumi genoset GO convert methylumi genoset
12.0 years ago Juan Fernández Tajes ▴ 190
0
votes
1
reply
2.1k
views
How to compare GO term lists and create matching network?
GO Network GUI Organism GO Network GUI Organism
updated 12.0 years ago by ▴ 750 • written 12.0 years ago by ▴ 160
0
votes
1
reply
1.3k
views
Differential gene expression of a cluster or group of genes
GO limma GO limma
updated 12.0 years ago by 53k • written 12.0 years ago by ▴ 240
0
votes
1
reply
1.9k
views
help: goseq and makeOrgPackageFromNCBI in AnnotationForge
RNASeq GO Organism AnnotationDbi goseq RNASeq GO Organism AnnotationDbi goseq
updated 12.0 years ago by ★ 7.2k • written 12.0 years ago by ▴ 80
0
votes
1
reply
1.4k
views
Retrieve GO terms for organism without complete genomes and do enrichment by myself
GO Organism GO Organism
updated 12.0 years ago by ★ 7.2k • written 12.0 years ago by ▴ 110
2
votes
2
replies
9.0k
views
package built under R version 3.1.0 warning
GO GO
updated 12.0 years ago by ★ 7.2k • written 12.0 years ago by ▴ 760
0
votes
1
reply
903
views
DEXSeq, gene not testable due to 2 out of 84 exons with a low nr of counts
GO GO
updated 12.0 years ago by ★ 3.8k • written 12.0 years ago by ▴ 20
0
votes
1
reply
1.0k
views
AnnotationHub resource down?
GO GO
updated 12.0 years ago by ★ 8.2k • written 12.0 years ago by 68k
0
votes
2
replies
4.8k
views
Annotate - gene name to ENSEMBL
Microarray GO lumi Microarray GO lumi
updated 12.0 years ago by ▴ 400 • written 12.0 years ago by ▴ 180
0
votes
0
replies
1.3k
views
Retrieve GO terms for unanontaded organism and do enrichment by myself
Proteomics GO Organism Proteomics GO Organism
12.0 years ago Ricardo Silva ▴ 110
0
votes
1
reply
1.3k
views
New GO terms after TopGO enrichment? (updated)
GO topGO GO topGO
updated 12.0 years ago by ▴ 160 • written 12.0 years ago by ▴ 400
1
vote
0
replies
1.2k
views
New GO terms after TopGO enrichment? (updated)
GO topGO GO topGO
12.0 years ago biotech ▴ 160
0
votes
0
replies
1.2k
views
New GO terms after TopGO enrichment?
GO topGO GO topGO
12.0 years ago biotech ▴ 160
0
votes
1
reply
1.6k
views
upload multiple genelists at a time for GO or pathway enrichment
GO cdf oligo pdInfoBuilder xps GO cdf oligo pdInfoBuilder xps
updated 12.0 years ago by ▴ 190 • written 12.0 years ago by ▴ 100
0
votes
1
reply
2.1k
views
Coercing matrix into expression set, for normalization of only subsets of miRNAs (affy miRNA3.0)
miRNA Normalization GO Biobase affy convert oligo miRNA Normalization GO Biobase affy
updated 12.0 years ago by ▴ 190 • written 12.0 years ago by 68k
0
votes
3
replies
1.4k
views
Rsubread featureCounts question
GO GO
updated 12.0 years ago by ★ 3.6k • written 12.1 years ago by 68k
0
votes
1
reply
779
views
Extracting genes associated to GO terms
GO ath1121501 GO ath1121501
updated 12.0 years ago by 68k • written 12.0 years ago by ★ 13k
0
votes
1
reply
845
views
Error in extracting genes from Goterms using GOStats package
GO GO
updated 12.0 years ago by 68k • written 12.0 years ago by ▴ 10
0
votes
1
reply
2.0k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
GO TranscriptDb goseq genomes GO TranscriptDb goseq genomes
updated 12.1 years ago by ★ 7.2k • written 12.1 years ago by ▴ 80
0
votes
6
replies
4.4k
views
Directed MST (Edmond's Algorithm)
GO graph RBGL GO graph RBGL
updated 12.1 years ago by ★ 13k • written 12.1 years ago by ▴ 90
0
votes
1
reply
2.5k
views
deseq2 plotMA
GO graph DESeq2 GO graph DESeq2
updated 12.1 years ago by 43k • written 12.1 years ago by ▴ 310
0
votes
3
replies
1.7k
views
edgeR adding RefSeq IDs
GO GO
updated 12.1 years ago by 68k • written 12.1 years ago by ★ 13k
0
votes
2
replies
3.6k
views
Biobase - Error: ExpressionSet
Microarray Annotation GO ExperimentData Biobase Microarray Annotation GO ExperimentData
updated 12.1 years ago by 1.6k • written 12.1 years ago by ▴ 50
0
votes
2
replies
1.9k
views
limma_3.17.23 - missing ILMN identifiers in EList objects after read.ilmn
Annotation Normalization GO probe annotate Annotation Normalization GO probe annotate
updated 12.1 years ago by ★ 3.6k • written 12.1 years ago by ▴ 120
0
votes
3
replies
2.6k
views
Getting GO ids for genenames in plasmodium falciparum
GO Plasmodium falciparum PROcess convert GO Plasmodium falciparum PROcess convert
updated 12.1 years ago by 25k • written 12.1 years ago by ★ 13k
0
votes
1
reply
1.9k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq GO Network rtracklayer CAMERA chipseq Gviz ChIPSeq GO Network rtracklayer Gviz
updated 12.1 years ago by ★ 11k • written 12.1 years ago by ▴ 40
0
votes
0
replies
1.4k
views
Measuring shifts in intronic expression independently of exons
GO DESeq DEXSeq ggbio GO DESeq DEXSeq ggbio
12.1 years ago James Perkins ▴ 60
0
votes
0
replies
1.4k
views
[devteam-bioc] Why does a GOAllFrame contain more rows than its argument GoFrame?
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
12.1 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
3.3k
views
GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
GO Visualization edgeR gage GO Visualization edgeR gage
12.1 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
1.1k
views
GOstats code validation
GO GO
updated 12.1 years ago by ▴ 10 • written 12.1 years ago by ★ 13k
0
votes
1
reply
1.2k
views
'AnnotationDbi' 1.23.24 is required by ‘GO.db’ in Windows
GO AnnotationDbi GO AnnotationDbi
updated 12.1 years ago by ★ 8.2k • written 12.1 years ago by ▴ 10
0
votes
1
reply
2.5k
views
problem with TXNAME -> SYMBOL mapping in Homo.sapiens library
GO GO
updated 12.1 years ago by ★ 7.2k • written 12.1 years ago by ★ 13k
0
votes
4
replies
1.9k
views
Measuring shifts in intronic expression independently of exons
GO DESeq DEXSeq ggbio GO DESeq DEXSeq ggbio
12.1 years ago James Perkins ▴ 60
0
votes
1
reply
1.6k
views
ChIPpeakAnno, getAnnotation question
Annotation GO zebrafish convert biomaRt ChIPpeakAnno Annotation GO zebrafish convert
updated 12.1 years ago by ★ 4.3k • written 12.1 years ago by ★ 13k
0
votes
5
replies
3.5k
views
Biostrings::matchPattern,extract sequences
GO BSgenome BSgenome GO BSgenome BSgenome
updated 12.2 years ago by 16k • written 12.2 years ago by ★ 4.3k
0
votes
10
replies
4.4k
views
problem while loading affycoretools
GO GO
updated 12.2 years ago by 68k • written 12.2 years ago by ▴ 510
0
votes
2
replies
3.9k
views
topGO issues
Annotation GO probe Annotation GO probe
updated 12.2 years ago by ★ 7.2k • written 12.2 years ago by ★ 13k
0
votes
3
replies
4.1k
views
How to deal with Affymetrix probe that map to multiple genes
GO Clustering probe convert GO Clustering probe convert
12.2 years ago Gundala Viswanath ▴ 230
0
votes
1
reply
1.1k
views
Exception thrown in ReadAffy() when reading Hu-133B files in a GEO Dataset
GO GO
updated 12.2 years ago by 21k • written 12.2 years ago by ▴ 90
0
votes
0
replies
2.6k
views
8. CGHCall problems (Bernard North [guest]) : Bioconductor Digest, Vol 126, Issue 7
aCGH RNASeq ChIPSeq Proteomics Annotation Normalization GO Network Cancer ChipName probe
12.2 years ago Sarah JugurnauthLittle ▴ 20
0
votes
2
replies
4.0k
views
getGmt error
GO hgu95a hgu95av2 GO hgu95a hgu95av2
updated 12.2 years ago by 25k • written 12.2 years ago by ★ 13k
0
votes
0
replies
1.7k
views
creating geneset files (.gmt) for GSEA
GO biomaRt GO biomaRt
12.2 years ago Nehme Hachem ▴ 20
1,936 results • Page 7 of 39
Recent ...
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Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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